OmniVira

Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe.

Chiara Rossi1 Nicola Zadra1 Cristina Fevola1,2 Frauke Ecke3 Birger Hörnfeldt3 René Kallies4 Maria Kazimirova5 Magnus Magnusson3 Gert E Olsson3,6 Rainer G Ulrich7 Anne J Jääskeläinen8 Heikki Henttonen9 Heidi C Hauffe1
Affiliations 9 institutions
  1. Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, TN, Italy.
  2. Department of Virology, Faculty of Medicine, University of Helsinki, FI-00029 Helsinki, Finland.
  3. Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
  4. Department of Environmental Microbiology Working Group Microbial Interaction Ecology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.
  5. Slovak Academy of Sciences (SAS), Institute of Zoology, 845 06 Bratislava, Slovakia.
  6. Unit for Nature Conservation, County Administrative Board of Halland County, 301 86 Halmstad, Sweden.
  7. Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany.
  8. HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, FI-00029 Helsinki, Finland.
  9. Wildlife Ecology, Natural Resources Institute Finland (LUKE), FI-00790 Helsinki, Finland.
PMID34372523 DOI10.3390/v13071317 Year2021 Journal Viruses Languageeng Statusepublish

Abstract

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5' untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.

Supporting text Virus Host Location
bank vole 2 Ljungan virus isolates 1 Parechovirus B 1 Picornaviridae 8 rodent-borne virus 2 small mammals 3 zoonosis 116 Evolution, Molecular 176 Host Specificity 132 Phylogeny 805 5' Untranslated Regions 4 Animals 1948 Europe 27 Genetic Variation 127 Genotype 137 Mammals 92 Parechovirus 1 Picornaviridae Infections 8

Evidence records

3 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE5055 Viral Detection
Key finding

Ljungan virus RNA was detected in 24 free-living small mammals across Europe.

Virus
Ljungan virus
Host
mammals Mammalia Natural host
Location
Europe
Supporting text

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region and the 3Dpol region from 24 LV RNA-positive animals.

Method
phylogenetic analysis | RNA detection | sequence analysis
Sample type
animal specimens
Geographic raw
Europe
Evidence type Reservoir Ecology
1 records
OVE5057 Reservoir Ecology
Key finding

Ljungan virus variants show host-specific associations among small mammal species within their European range.

Virus
Ljungan virus
Host
mammals Mammalia Natural host
Location
Europe
Supporting text

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. There are several other indications that LV variants are host-specific, at least in parts of their range.

Method
phylogenetic comparison of VP1 and 3Dpol regions
Sample type
RNA-positive animals
Geographic raw
Europe
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE5056 Phylogenetic Evolution
Key finding

Phylogenetic analysis of VP1 sequences identified three new Ljungan virus genotypes, with genotype 7 in field voles (Microtus arvalis) and genotypes 8 and 9 in bank voles (Myodes glareolus) across several European countries.

Virus
Ljungan virus
Host
Bank vole Myodes glareolus Natural host common vole Microtus arvalis Natural host
Location
Not specified
Supporting text

We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland).

Genes or proteins
VP1
Analysis methods
phylogenetic analysis